Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005930.1 Hibiscus syriacus cultivar Beakdansim tig00013920_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 177149
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1722 original size:19 final size:19
Alignment explanation
Indices: 1695--1744 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1685 TCATTGTAGT
1695 TGTTATTTGCTATGATCCA
1 TGTTATTTGCTATGATCCA
* *
1714 TGTTTTTTGCCATGATCCA
1 TGTTATTTGCTATGATCCA
1733 TGTTATTTGCTA
1 TGTTATTTGCTA
1745 ACCATTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (19 bp):
TGTTATTTGCTATGATCCA
Found at i:6017 original size:21 final size:20
Alignment explanation
Indices: 5992--6035 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
5982 TAAATATTTT
*
5992 TTAATTCAAAAAAGTTTATAA
1 TTAATTCAAAAAA-TATATAA
* *
6013 TTAATTTAAATAATATATAA
1 TTAATTCAAAAAATATATAA
6033 TTA
1 TTA
6036 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATTCAAAAAATATATAA
Found at i:22270 original size:23 final size:22
Alignment explanation
Indices: 22198--22279 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 22
22188 ATACTGAACA
22198 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CC-TTGAAT
** *
22222 GTGCATCGATAAAT-CATGAA-
1 GTGCATCGATGCATCCTTGAAT
22242 GATGCATCGATGCACTCCTTGAAT
1 G-TGCATCGATGCA-TCCTTGAAT
22266 GTGCATCGATGCAT
1 GTGCATCGATGCAT
22280 TTGTCGGGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 14 0.29
22 3 0.06
23 17 0.35
24 13 0.27
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:28396 original size:11 final size:10
Alignment explanation
Indices: 28362--28395 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
28352 ATTAAAATTA
28362 AAAAATATAT
1 AAAAATATAT
*
28372 AATAATAT-T
1 AAAAATATAT
28381 AAAAATATAT
1 AAAAATATAT
28391 AAAAA
1 AAAAA
28396 AATTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATATAT
Found at i:28406 original size:19 final size:19
Alignment explanation
Indices: 28355--28399 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
28345 ATTTTTTATT
*
28355 AAAATTAAAAAATATATAAT
1 AAAATT-AAAAATATATAAA
*
28375 AATATTAAAAATATATAAA
1 AAAATTAAAAATATATAAA
28394 AAAATT
1 AAAATT
28400 TGAAATAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAATATATAAA
Found at i:35508 original size:2 final size:2
Alignment explanation
Indices: 35501--35590 Score: 171
Period size: 2 Copynumber: 45.0 Consensus size: 2
35491 AATTAACACA
35501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35585 AT AT AT
1 AT AT AT
35591 TAAATCACGA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35992 original size:2 final size:2
Alignment explanation
Indices: 35985--36016 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35975 ATATTCTCTA
35985 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36017 TCAATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36214 original size:53 final size:53
Alignment explanation
Indices: 36122--36328 Score: 245
Period size: 53 Copynumber: 3.9 Consensus size: 53
36112 TTTTATGTAT
*
36122 TAAGATATTGAGAGATATACATACTAACACTGGTGTAAGTATGTGTTAATTGC
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
* * ** *
36175 CAAGATATTGAGAGATATACATACTTACATCT-GTATAAGTATGCATTAATTTC
1 TAAGATATTGAGAGATATACATACTTACA-CTGGTGTAAGTATGTGTTAATTGC
* * ** *
36228 TAAGATATTGAGAGATGTACATAATTACACTGGTGTAAGTACATGTTAATTGT
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
* * * * * *
36281 TAAGATATTTAGAGATGTACATACTTATACCGGTGTAAATAAGTGTTA
1 TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTA
36329 GTTGATATAT
Statistics
Matches: 129, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
52 2 0.02
53 125 0.97
54 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (53 bp):
TAAGATATTGAGAGATATACATACTTACACTGGTGTAAGTATGTGTTAATTGC
Found at i:36548 original size:6 final size:6
Alignment explanation
Indices: 36532--36566 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
36522 ATAAATACTC
36532 AAAAT- AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
36567 CTAATGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:38894 original size:12 final size:12
Alignment explanation
Indices: 38877--40022 Score: 1889
Period size: 12 Copynumber: 95.6 Consensus size: 12
38867 GACTCTATTT
38877 TACATACATACA
1 TACATACATACA
38889 TACATACATACA
1 TACATACATACA
38901 TACATACATACA
1 TACATACATACA
38913 TACATACATACA
1 TACATACATACA
38925 TACATACATACA
1 TACATACATACA
38937 TACATACATACA
1 TACATACATACA
*
38949 TACATACATATA
1 TACATACATACA
* *
38961 TATATATATACA
1 TACATACATACA
* *
38973 TATATACGTACA
1 TACATACATACA
*
38985 TACATACGTACA
1 TACATACATACA
*
38997 TACATACGTACA
1 TACATACATACA
*
39009 TACATACGTACA
1 TACATACATACA
*
39021 TACATACGTACA
1 TACATACATACA
*
39033 TACATACGTACA
1 TACATACATACA
* *
39045 TATATACGTACA
1 TACATACATACA
*
39057 TACATACGTACA
1 TACATACATACA
*
39069 TACATACGTACA
1 TACATACATACA
*
39081 TACATACGTACA
1 TACATACATACA
*
39093 TACATACGTACA
1 TACATACATACA
*
39105 TACATACGTACA
1 TACATACATACA
*
39117 TACATACGTACA
1 TACATACATACA
39129 TACATACATACA
1 TACATACATACA
* *
39141 TACGTACGTACA
1 TACATACATACA
39153 TACATACATACA
1 TACATACATACA
39165 TACATACATACA
1 TACATACATACA
*
39177 TACATACGTACA
1 TACATACATACA
39189 TACATACATACA
1 TACATACATACA
39201 TACATACATACA
1 TACATACATACA
39213 TACATACATACA
1 TACATACATACA
39225 TACATACATACA
1 TACATACATACA
39237 TACATACATACA
1 TACATACATACA
39249 TACATACATACA
1 TACATACATACA
39261 TACATACATACA
1 TACATACATACA
39273 TACATACATACA
1 TACATACATACA
39285 TACATACATACA
1 TACATACATACA
39297 TACATACATACA
1 TACATACATACA
39309 TACATACATACA
1 TACATACATACA
39321 TACATACATACA
1 TACATACATACA
39333 TACATACATACA
1 TACATACATACA
39345 TACATACATACA
1 TACATACATACA
39357 TACATACATACA
1 TACATACATACA
39369 TACATACATACA
1 TACATACATACA
39381 TACATACATACA
1 TACATACATACA
39393 TACATACATACA
1 TACATACATACA
39405 TACATACATACA
1 TACATACATACA
39417 TACATACATACA
1 TACATACATACA
*
39429 TATATACATACA
1 TACATACATACA
39441 TACATACATACA
1 TACATACATACA
*
39453 TACATACGTACA
1 TACATACATACA
*
39465 TACATACGTACA
1 TACATACATACA
*
39477 TACATACGTACA
1 TACATACATACA
*
39489 TACATACGTACA
1 TACATACATACA
*
39501 TACATACGTACA
1 TACATACATACA
*
39513 TACATACGTACA
1 TACATACATACA
*
39525 TACATACGTACA
1 TACATACATACA
*
39537 TACATACGTACA
1 TACATACATACA
39549 TACATACATACA
1 TACATACATACA
* **
39561 TATATATGTACA
1 TACATACATACA
**
39573 TACATACATATG
1 TACATACATACA
39585 TACATACATACA
1 TACATACATACA
** *
39597 TATGTATATACA
1 TACATACATACA
*
39609 TACATACGTACA
1 TACATACATACA
*
39621 TACATACATACG
1 TACATACATACA
39633 TACATACATACA
1 TACATACATACA
39645 TACATACATACA
1 TACATACATACA
39657 TACATACATACA
1 TACATACATACA
39669 TACATACATACA
1 TACATACATACA
39681 TACATACATACA
1 TACATACATACA
39693 TACATACATACA
1 TACATACATACA
39705 TACATACATACA
1 TACATACATACA
39717 TACATACATACA
1 TACATACATACA
39729 TACATACATACA
1 TACATACATACA
39741 TACATACATACA
1 TACATACATACA
39753 TACATACATACA
1 TACATACATACA
39765 TAC-TACATACA
1 TACATACATACA
39776 TACATACATACA
1 TACATACATACA
39788 TACATACATACA
1 TACATACATACA
39800 TACATACATACA
1 TACATACATACA
39812 TACATACATACA
1 TACATACATACA
39824 TACATACATACA
1 TACATACATACA
39836 TACATACATACA
1 TACATACATACA
39848 TACATACATACA
1 TACATACATACA
39860 TACATACATACA
1 TACATACATACA
39872 TACATACATACA
1 TACATACATACA
* *
39884 TACGTACATACG
1 TACATACATACA
*
39896 TACATACGTACA
1 TACATACATACA
39908 TACATACATACA
1 TACATACATACA
*
39920 TACATACATACG
1 TACATACATACA
39932 TACATACATACA
1 TACATACATACA
39944 TACATACATACA
1 TACATACATACA
39956 TACATACATACA
1 TACATACATACA
39968 TACATACATACA
1 TACATACATACA
39980 TACATACATACA
1 TACATACATACA
39992 TACATACATACA
1 TACATACATACA
40004 TACATACATACA
1 TACATACATACA
40016 TACATAC
1 TACATAC
40023 TAAATTATAG
Statistics
Matches: 1085, Mismatches: 48, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
11 11 0.01
12 1074 0.99
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (12 bp):
TACATACATACA
Found at i:40180 original size:12 final size:13
Alignment explanation
Indices: 40164--40196 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
40154 ATTATTATCT
40164 AAAAATAATTTTA
1 AAAAATAATTTTA
40177 AAAAATAA-TTTA
1 AAAAATAATTTTA
40189 AATAAATA
1 AA-AAATA
40197 TATTAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:40262 original size:17 final size:16
Alignment explanation
Indices: 40240--40294 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
40230 CTCTAAATAA
40240 TTTTAATATGATTTTAT
1 TTTTAATAT-ATTTTAT
40257 TTTTAATATATTTTAT
1 TTTTAATATATTTTAT
*
40273 ATATTT-TTAT-TTTTAT
1 -T-TTTAATATATTTTAT
40289 TTTTAA
1 TTTTAA
40295 ATAAAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 13 0.39
17 13 0.39
18 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTTAATATATTTTAT
Found at i:40264 original size:26 final size:26
Alignment explanation
Indices: 40235--40287 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
40225 GAATTCTCTA
40235 AATA-ATTTTA-ATATGATTTTATTTTT
1 AATATATTTTATATAT--TTTTATTTTT
40261 AATATATTTTATATATTTTTATTTTT
1 AATATATTTTATATATTTTTATTTTT
40287 A
1 A
40288 TTTTTAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 15 0.60
27 6 0.24
28 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
AATATATTTTATATATTTTTATTTTT
Found at i:42938 original size:3 final size:3
Alignment explanation
Indices: 42930--42964 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
42920 ATTTAAATAC
42930 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42965 TACAGGAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:47126 original size:35 final size:35
Alignment explanation
Indices: 47080--47155 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
47070 TTAGATTCAT
* *
47080 TTCAACTTTATCTTGGAAATCACTCTCTTGTTAAC
1 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
47115 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
1 TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
47150 TTCAAC
1 TTCAAC
47156 CCAGAACCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.41
Consensus pattern (35 bp):
TTCAACTTTATCTTGAAAACCACTCTCTTGTTAAC
Found at i:51629 original size:26 final size:27
Alignment explanation
Indices: 51581--51636 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
51571 AAACCCCTAG
*
51581 AAATATGTTTAGGGGTTTTTCCTATTT
1 AAATAGGTTTAGGGGTTTTTCCTATTT
51608 AAATAGGTTTA-GGGTTTTTCCTATTT
1 AAATAGGTTTAGGGGTTTTTCCTATTT
51634 AAA
1 AAA
51637 GTTCTTTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (27 bp):
AAATAGGTTTAGGGGTTTTTCCTATTT
Found at i:54290 original size:21 final size:21
Alignment explanation
Indices: 54264--54337 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
54254 CCCTAAATAC
54264 CACATATATGTTCCAAAGGAT
1 CACATATATGTTCCAAAGGAT
*
54285 CACATATATGTTCCAAAGGAC
1 CACATATATGTTCCAAAGGAT
** *
54306 CGTATATATGTTCCAAATGAT
1 CACATATATGTTCCAAAGGAT
*
54327 CACTTATATGT
1 CACATATATGT
54338 CTCGAATGAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (21 bp):
CACATATATGTTCCAAAGGAT
Found at i:66788 original size:16 final size:16
Alignment explanation
Indices: 66767--66800 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
66757 TGTCACGTCT
66767 ATATTTTCTTTAAAAA
1 ATATTTTCTTTAAAAA
* *
66783 ATATTTTTTTTTAAAA
1 ATATTTTCTTTAAAAA
66799 AT
1 AT
66801 TTGGACGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTCTTTAAAAA
Found at i:82598 original size:15 final size:16
Alignment explanation
Indices: 82570--82601 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
82560 AAAATCTTTC
82570 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
82586 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
82601 T
1 T
82602 GGATCTTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.50
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:85059 original size:24 final size:22
Alignment explanation
Indices: 84999--85059 Score: 104
Period size: 22 Copynumber: 2.7 Consensus size: 22
84989 CGTTATTGGA
84999 GTTTCTTATATTTTCCTAATTT
1 GTTTCTTATATTTTCCTAATTT
85021 GTTTCTTATATTTTCCTAATTT
1 GTTTCTTATATTTTCCTAATTT
85043 GTTTCTGATATATTTTC
1 GTTTCT--TATATTTTC
85060 GGATGTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 28 0.76
24 9 0.24
ACGTcount: A:0.18, C:0.13, G:0.07, T:0.62
Consensus pattern (22 bp):
GTTTCTTATATTTTCCTAATTT
Found at i:91026 original size:31 final size:32
Alignment explanation
Indices: 90988--91054 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
90978 AAAAAATTTA
*
90988 TTTGTATTTATG-CTAGTACTTGGCTTGCCGT
1 TTTGTATTTATGCCAAGTACTTGGCTTGCCGT
*
91019 TTTGTATTTATGCCAAGTATTTGGCTTGCCGT
1 TTTGTATTTATGCCAAGTACTTGGCTTGCCGT
91051 TTTG
1 TTTG
91055 CTTTAGAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 12 0.36
32 21 0.64
ACGTcount: A:0.13, C:0.15, G:0.22, T:0.49
Consensus pattern (32 bp):
TTTGTATTTATGCCAAGTACTTGGCTTGCCGT
Found at i:93981 original size:21 final size:20
Alignment explanation
Indices: 93957--94011 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 20
93947 ATTAAATATC
93957 TTATACATAAACTTA-ACTAAT
1 TTATACATAAACTTACAC--AT
*
93978 TTATAAGATAAAC-TACACAT
1 TTAT-ACATAAACTTACACAT
93998 TTAATACATAAACT
1 TT-ATACATAAACT
94012 ATTAGTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 11 0.39
21 8 0.29
22 9 0.32
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.35
Consensus pattern (20 bp):
TTATACATAAACTTACACAT
Found at i:96203 original size:13 final size:13
Alignment explanation
Indices: 96185--96210 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96175 TCCAAGTAGT
96185 GGAAGCCCTTGCA
1 GGAAGCCCTTGCA
96198 GGAAGCCCTTGCA
1 GGAAGCCCTTGCA
96211 CAAAAAGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
GGAAGCCCTTGCA
Found at i:96676 original size:14 final size:17
Alignment explanation
Indices: 96645--96676 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
96635 ATCCTAGATT
96645 ATATTATTAATAGAAAA
1 ATATTATTAATAGAAAA
96662 ATATT-TTAAT-GAAAA
1 ATATTATTAATAGAAAA
96677 CGTATAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 5 0.33
17 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (17 bp):
ATATTATTAATAGAAAA
Found at i:105143 original size:33 final size:35
Alignment explanation
Indices: 105097--105166 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 35
105087 TTTAGCTTGG
105097 AAATAAATATGTTT-CCAAAACTAAATGAAT-ATT
1 AAATAAATATGTTTGCCAAAACTAAATGAATGATT
* ** *
105130 AAATAAATTTGTTTGCGGACACTAAATGAATGATT
1 AAATAAATATGTTTGCCAAAACTAAATGAATGATT
105165 AA
1 AA
105167 CGAATATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 13 0.42
34 13 0.42
35 5 0.16
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (35 bp):
AAATAAATATGTTTGCCAAAACTAAATGAATGATT
Found at i:115814 original size:133 final size:133
Alignment explanation
Indices: 115576--115841 Score: 532
Period size: 133 Copynumber: 2.0 Consensus size: 133
115566 GCGATTTTCT
115576 CGATATATCACTGGTGAACAGTATATTTTTTGATCTAACACCGGTCAGATTATATTTATCGATCT
1 CGATATATCACTGGTGAACAGTATATTTTTTGATCTAACACCGGTCAGATTATATTTATCGATCT
115641 AACACCCATAGTAGTAAAGCGCACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGAT
66 AACACCCATAGTAGTAAAGCGCACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGAT
115706 ATA
131 ATA
115709 CGATATATCACTGGTGAACAGTATATTTTTTGATCTAACACCGGTCAGATTATATTTATCGATCT
1 CGATATATCACTGGTGAACAGTATATTTTTTGATCTAACACCGGTCAGATTATATTTATCGATCT
115774 AACACCCATAGTAGTAAAGCGCACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGAT
66 AACACCCATAGTAGTAAAGCGCACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGAT
115839 ATA
131 ATA
115842 GCGGGCCCCC
Statistics
Matches: 133, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 133 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (133 bp):
CGATATATCACTGGTGAACAGTATATTTTTTGATCTAACACCGGTCAGATTATATTTATCGATCT
AACACCCATAGTAGTAAAGCGCACCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGAT
ATA
Found at i:115884 original size:53 final size:51
Alignment explanation
Indices: 115797--115954 Score: 237
Period size: 53 Copynumber: 3.0 Consensus size: 51
115787 GTAAAGCGCA
*
115797 CCCCTGCACCGCGCTATACGATGATTTGGCACCACGTGGGATATAGCGGGC
1 CCCCTACACCGCGCTATACGATGATTTGGCACCACGTGGGATATAGCGGGC
115848 CCCCTACACCGCGCTATACACGATGATTTGGCACCACGTGGGATATAGCGGGC
1 CCCCTACACCGCGCTAT--ACGATGATTTGGCACCACGTGGGATATAGCGGGC
* * *
115901 CCCCTACACCGCGCTATACGGTGATCTGGCATACACGTGGG-TATAGCGCGGC
1 CCCCTACACCGCGCTATACGATGATTTGGCA-CCACGTGGGATATAGCG-GGC
115953 CC
1 CC
115955 TTGCAGCGCT
Statistics
Matches: 99, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
51 35 0.35
52 13 0.13
53 51 0.52
ACGTcount: A:0.20, C:0.33, G:0.28, T:0.19
Consensus pattern (51 bp):
CCCCTACACCGCGCTATACGATGATTTGGCACCACGTGGGATATAGCGGGC
Found at i:116052 original size:21 final size:21
Alignment explanation
Indices: 116028--116075 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
116018 TCACGTCTCC
116028 ATCCTCCCGATAAATACCCCA
1 ATCCTCCCGATAAATACCCCA
* *
116049 ATCCTCCCTATAAATACCCCC
1 ATCCTCCCGATAAATACCCCA
116070 ATCCTC
1 ATCCTC
116076 AATCACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.46, G:0.02, T:0.23
Consensus pattern (21 bp):
ATCCTCCCGATAAATACCCCA
Found at i:116134 original size:12 final size:10
Alignment explanation
Indices: 116093--116133 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
116083 TTTATCACAC
116093 CAAATTCTCT
1 CAAATTCTCT
116103 CAAATTCTCT
1 CAAATTCTCT
116113 -AAATTTCTCT
1 CAAA-TTCTCT
*
116123 CAAATACTCT
1 CAAATTCTCT
116133 C
1 C
116134 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:118211 original size:23 final size:22
Alignment explanation
Indices: 118185--118248 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
118175 CAACTCATAT
118185 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* *
118208 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
118231 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
118249 TATAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:118383 original size:103 final size:103
Alignment explanation
Indices: 118256--118481 Score: 416
Period size: 103 Copynumber: 2.2 Consensus size: 103
118246 CCATATAATA
* *
118256 ATGTCCAGAAGGACCACATATCATTCCTTAATAATCAAATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCAAATACATATGCCAAGGATCAAGTATGTG
118321 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
*
118359 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTG
1 ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCAAATACATATGCCAAGGATCAAGTATGTG
118424 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
*
118462 ATGTCCCGAAGGACCCCATA
1 ATGTCCCGAAGGACCACATA
118482 GACCCTCTAC
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 119 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (103 bp):
ATGTCCCGAAGGACCACATATCATTCCTTAAGAATCAAATACATATGCCAAGGATCAAGTATGTG
TCTCACCAGACCTCACACATGTTCCAAAGAATACATAT
Found at i:119045 original size:64 final size:67
Alignment explanation
Indices: 118930--119057 Score: 183
Period size: 64 Copynumber: 2.0 Consensus size: 67
118920 ATTTTCATCT
*
118930 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCAATGCATAAATCCTATTTGATGTTTG
1 TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCAATGCATAAATCCTATTCGATGTTTG
118995 TA
66 TA
* * *
118997 TTTAATGG-GG-ATGCATCGATGCACT-C-CTTATGCATCGATGTATAAATCCTATTCGATGTTT
1 TTTAATGGAGGTATGCATCGATGCACTACAC-CATGCATCAATGCATAAATCCTATTCGATGTTT
119058 TCTTTTTAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
63 1 0.02
64 30 0.54
65 15 0.27
66 2 0.04
67 8 0.14
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (67 bp):
TTTAATGGAGGTATGCATCGATGCACTACACCATGCATCAATGCATAAATCCTATTCGATGTTTG
TA
Found at i:119075 original size:64 final size:62
Alignment explanation
Indices: 118942--119102 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 62
118932 TAATGGAGGT
* * * * *
118942 ATGCATCGATGCACTACACCATGCATCAATGCATAAATCCTATTTGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
119007 ATGCATCGATGCACTCCTTATGCATCGATGTATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
119071 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
119103 CCTTAAACAA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
63 1 0.01
64 54 0.67
65 23 0.28
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.35
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:122499 original size:50 final size:50
Alignment explanation
Indices: 122386--122509 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
122376 CCCTACGTGG
* * *
122386 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGTATGCCAGATCAC
1 CGTATAGCGCGGTGCAGGGG-CGCGCTATACCCACGTGTACGCCAAATCAC
* * * *
122437 CATATAGCGCGGTGCAGGGGCGTGCTATACCCCACGTG-GCGCCAAATCAT
1 CGTATAGCGCGGTGCAGGGGCGCGCTATA-CCCACGTGTACGCCAAATCAC
*
122487 CGTATAACGCGGTGCAGGGGCGC
1 CGTATAGCGCGGTGCAGGGGCGC
122510 ACTTTACTGC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 36 0.58
51 26 0.42
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (50 bp):
CGTATAGCGCGGTGCAGGGGCGCGCTATACCCACGTGTACGCCAAATCAC
Found at i:122820 original size:31 final size:31
Alignment explanation
Indices: 122784--122844 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
122774 AACATAATAT
*
122784 ATAATCACTTTTATTTTTATTTAGTTAAGAA
1 ATAATCACTTTTATTTTTATTTAATTAAGAA
*
122815 ATAATCACTTTTGTTTTTATTTAATTAAGA
1 ATAATCACTTTTATTTTTATTTAATTAAGA
122845 TGTGATAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (31 bp):
ATAATCACTTTTATTTTTATTTAATTAAGAA
Found at i:123445 original size:18 final size:18
Alignment explanation
Indices: 123422--123457 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
123412 ATCATGTCTT
123422 AATTAAATAAAAATGAAA
1 AATTAAATAAAAATGAAA
123440 AATTAAATAAAAATGAAA
1 AATTAAATAAAAATGAAA
123458 GTGACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (18 bp):
AATTAAATAAAAATGAAA
Found at i:124478 original size:18 final size:18
Alignment explanation
Indices: 124451--124501 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
124441 GGAATGTTTA
*
124451 TGAAGAAATTGGAATCTG
1 TGAAGGAATTGGAATCTG
*
124469 TGAAGGAATTGGAATATG
1 TGAAGGAATTGGAATCTG
*
124487 T--AGGAATTTGAATCT
1 TGAAGGAATTGGAATCT
124502 AATTTCATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 12 0.41
18 17 0.59
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (18 bp):
TGAAGGAATTGGAATCTG
Found at i:124799 original size:33 final size:34
Alignment explanation
Indices: 124754--124832 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 34
124744 AATAAACCCG
*
124754 AACCCGACCCGACCCGAATATTACACTT-AAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAA
* *
124787 AATCCGACCCGACTCGAATATCACACTTAAAAAA
1 AACCCGACCCGACCCGAATATCACACTTAAAAAA
124821 AACCCGACCCGA
1 AACCCGACCCGA
124833 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 25 0.61
34 16 0.39
ACGTcount: A:0.42, C:0.34, G:0.10, T:0.14
Consensus pattern (34 bp):
AACCCGACCCGACCCGAATATCACACTTAAAAAA
Found at i:125179 original size:210 final size:213
Alignment explanation
Indices: 124790--125315 Score: 713
Period size: 210 Copynumber: 2.4 Consensus size: 213
124780 TTAAAAAAAT
* * *
124790 CCGACCCGACTCGAATATCACACTTAAAAAA---AACCCGACCCGAACAAAATAAAGTTTCATCC
1 CCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAG-TT--T-C
** * *
124852 GATCCGACCCGAATATATGAATTAGAAATCTGACCCGACCCGACCCGAAATAATAAAAAATTATT
62 -ATCCGACCCGAATATATGAATTAGAAATCCAAACCGACCCGACCCGAAATAATAAAAAAATATT
* *
124917 TTTATTTAATAAAAACAGTGACTTAATCCTACCCGACCCGAATTATATATATTTTTGGGTCGGTC
126 TTTATTTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTTGGGTCGGTC
* *
124982 CGGTTTTTTT-C-ACTCTAA-AC
191 CGGTTTTTTTCCAACCCGAACAC
*
125002 CCGACTCGACCCAAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
1 CCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
125067 GACCCGAATATATGAATTAGAAATCCAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTAT
66 GACCCGAATATATGAATTAGAAATCCAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTAT
* *
125132 TTAATAAAAACAATGACTTAATCCAACCCGACCTGAATTATATATATTTTTGGGTCGGTCTGGTT
131 TTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTTGGGTCGGTCCGGTT
125197 TTTTTACCCTAAACCCGAACCCGAC
196 TTTTT--CC--AACCCGAA--C-AC
* * * * *
125222 CCGACCCGACCCAAATATCACACTTAAAAAAACCCGATCCAACTCGACCAAAATAAAGTTTCACC
1 CCGACCCGACCCAAATATCACACTT-AAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATC
*
125287 CGACCCGAATATATGAATTAGAAACCCAA
65 CGACCCGAATATATGAATTAGAAATCCAA
125316 CCCAAAATAA
Statistics
Matches: 279, Mismatches: 21, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
210 131 0.47
211 1 0.00
212 29 0.10
213 1 0.00
214 2 0.01
215 22 0.08
216 5 0.02
220 26 0.09
221 62 0.22
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.24
Consensus pattern (213 bp):
CCGACCCGACCCAAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAGTTTCATCC
GACCCGAATATATGAATTAGAAATCCAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTAT
TTAATAAAAACAATGACTTAATCCAACCCGACCCGAATTATATATATTTTTGGGTCGGTCCGGTT
TTTTTCCAACCCGAACAC
Found at i:125543 original size:2 final size:2
Alignment explanation
Indices: 125536--125561 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
125526 ACCAAACGCC
125536 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
125562 TACAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127197 original size:60 final size:59
Alignment explanation
Indices: 127066--127197 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 59
127056 AATAAAAAAT
* * *
127066 AATCATTTTAAAACTTTTAATAATCAAGAAATTTAATAAAATAACATTCTATAATTAAA
1 AATCATTTTATAACATTTAATAATCAAGAAATTTAATAAAATAACATCCTATAATTAAA
* * *
127125 AGATTATTTTATAACATTTAATAATCAATAAATTTAATAAAATAATATCCTATAATTAAA
1 A-ATCATTTTATAACATTTAATAATCAAGAAATTTAATAAAATAACATCCTATAATTAAA
127185 AATCATTCTTATA
1 AATCATT-TTATA
127198 CTTTACCCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
59 6 0.09
60 58 0.91
ACGTcount: A:0.51, C:0.08, G:0.02, T:0.39
Consensus pattern (59 bp):
AATCATTTTATAACATTTAATAATCAAGAAATTTAATAAAATAACATCCTATAATTAAA
Found at i:134773 original size:31 final size:31
Alignment explanation
Indices: 134738--134807 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
134728 CAACAGGTTG
134738 ATATCTTAAATAAATAAAAAC-AAATATGATC
1 ATATCTTAAATAAATAAAAACGAAA-ATGATC
*
134769 ATATCTTAATTAAATAAAAACGAAAATGATC
1 ATATCTTAAATAAATAAAAACGAAAATGATC
134800 ATATCTTA
1 ATATCTTA
134808 TATATTTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.31
Consensus pattern (31 bp):
ATATCTTAAATAAATAAAAACGAAAATGATC
Found at i:136376 original size:15 final size:15
Alignment explanation
Indices: 136353--136383 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
136343 CGGCCTTCCA
*
136353 GGCGGCTTCACGCTC
1 GGCGACTTCACGCTC
136368 GGCGACTTCACGCTC
1 GGCGACTTCACGCTC
136383 G
1 G
136384 CGTTCCTCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.10, C:0.39, G:0.32, T:0.19
Consensus pattern (15 bp):
GGCGACTTCACGCTC
Found at i:142643 original size:15 final size:16
Alignment explanation
Indices: 142613--142645 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
142603 AAAATCTTTC
*
142613 TTTCCCGTTTTGGATT
1 TTTCCCGTTCTGGATT
142629 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
142644 TT
1 TT
142646 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.21, G:0.18, T:0.55
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:144363 original size:19 final size:19
Alignment explanation
Indices: 144330--144385 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
144320 TTTCTCATTA
* *
144330 TGACTT-TGATCAAGGCTT
1 TGACTTCTGATGAAGGATT
144348 TGACTTCTGATGAAGGATT
1 TGACTTCTGATGAAGGATT
144367 TGACTTCTGATGAAGGATT
1 TGACTTCTGATGAAGGATT
144386 CCATCTATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
18 6 0.17
19 29 0.83
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (19 bp):
TGACTTCTGATGAAGGATT
Found at i:157396 original size:29 final size:25
Alignment explanation
Indices: 157353--157414 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 25
157343 AAAACAAAAT
157353 ATTTTATTTAAAAAATCATTTGAATTAA
1 ATTTTATTTAAAAAAT-ATTT--ATTAA
*
157381 ATTTTAATTTATAAAATATTTATTAA
1 ATTTT-ATTTAAAAAATATTTATTAA
157407 ATTATTAT
1 ATT-TTAT
157415 GAAATGGTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 10 0.32
27 2 0.06
28 9 0.29
29 10 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTATTTAAAAAATATTTATTAA
Found at i:160162 original size:32 final size:32
Alignment explanation
Indices: 160123--160185 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
160113 CATTTTTACA
* *
160123 AATAATTTGATTAAATTTATTAACCATTTTGT
1 AATAATTTGATAAAATTTAATAACCATTTTGT
*
160155 AATAATTTGATAAAATTTAATGACCATTTTG
1 AATAATTTGATAAAATTTAATAACCATTTTG
160186 ATAACATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (32 bp):
AATAATTTGATAAAATTTAATAACCATTTTGT
Found at i:161914 original size:57 final size:57
Alignment explanation
Indices: 161842--161950 Score: 218
Period size: 57 Copynumber: 1.9 Consensus size: 57
161832 GAGTATCCAT
161842 ACTTACCTCACTATCGAAAATATTAATTTAGGGTTATCTTTTGAGTGAGTTTTAAGA
1 ACTTACCTCACTATCGAAAATATTAATTTAGGGTTATCTTTTGAGTGAGTTTTAAGA
161899 ACTTACCTCACTATCGAAAATATTAATTTAGGGTTATCTTTTGAGTGAGTTT
1 ACTTACCTCACTATCGAAAATATTAATTTAGGGTTATCTTTTGAGTGAGTTT
161951 CAATACATTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (57 bp):
ACTTACCTCACTATCGAAAATATTAATTTAGGGTTATCTTTTGAGTGAGTTTTAAGA
Found at i:162447 original size:75 final size:75
Alignment explanation
Indices: 162347--162679 Score: 366
Period size: 75 Copynumber: 4.4 Consensus size: 75
162337 CTTAACCGGT
* * * *
162347 TAAAATAAAAT-AGACACTACTTATTATGTTAAACTACCTACCGGTTTGTTTAAATGTTACTAAT
1 TAAAATAAAATAAG-CGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAAT
*
162411 AATGTAAATGA
65 AATGTAAACGA
* * * * * * *
162422 TAAAATAAAATAAGCGTTACCTATTACGTTAAAATACTTATCAGTTTGTTTAAAGATTACTAATA
1 TAAAATAAAATAAGCGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
162487 ATGTAAA-GA
66 ATGTAAACGA
* * *
162496 GTAAAATAAAAT-AGACACTACATATTACGTTAAATTATCTACCGGTTTGTTTAAAGGTTACTAA
1 -TAAAATAAAATAAG-CGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAA
*
162560 TAATGTAAACGG
64 TAATGTAAACGA
* * * * * * *
162572 TAAAATAAAACAGGCGTTACCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATTATA
1 TAAAATAAAATAAGCGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
* *
162637 AGGTAAACGG
66 ATGTAAACGA
* * *
162647 TAAAATAAAATAGGTGCTACATATTATGTTAAA
1 TAAAATAAAATAAGCGCTACATATTACGTTAAA
162680 TAGGCGCTAC
Statistics
Matches: 218, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
74 4 0.02
75 210 0.96
76 4 0.02
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAAGCGCTACATATTACGTTAAACTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGA
Found at i:162619 original size:150 final size:150
Alignment explanation
Indices: 162347--162680 Score: 465
Period size: 150 Copynumber: 2.2 Consensus size: 150
162337 CTTAACCGGT
* * *
162347 TAAAATAAAATAGACACTACTTATTATGTTAAACTACCTACCGGTTTGTTTAAATGTTACTAATA
1 TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
* * *
162412 ATGTAAATGATAAAATAAAATAAGCGTTACCTATTACGTTAAAATACTTATCAGTTTGTTTAAAG
66 ATGTAAACGATAAAATAAAACAAGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAAAG
* *
162477 ATTACTAATAATGTAAA-GAG
131 ATTAATAATAAGGTAAACG-G
* *
162497 TAAAATAAAATAGACACTACATATTACGTTAAATTATCTACCGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
* * * *
162562 ATGTAAACGGTAAAATAAAACAGGCGTTACCTATTACGTTAAACTAAC-TACCGGTTTGTTTAAA
66 ATGTAAACGATAAAATAAAACAAGCGTTACCTATTACGTTAAAAT-ACTTACCAGTTTGTTTAAA
* *
162626 GGTTAATTATAAGGTAAACGG
130 GATTAATAATAAGGTAAACGG
***
162647 TAAAATAAAATAGGTGCTACATATTATGTTAAAT
1 TAAAATAAAATAGACACTACATATTATGTTAAAT
162681 AGGCGCTACA
Statistics
Matches: 162, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
150 159 0.98
151 3 0.02
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (150 bp):
TAAAATAAAATAGACACTACATATTATGTTAAATTACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGATAAAATAAAACAAGCGTTACCTATTACGTTAAAATACTTACCAGTTTGTTTAAAG
ATTAATAATAAGGTAAACGG
Found at i:162680 original size:23 final size:23
Alignment explanation
Indices: 162654--162718 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
162644 CGGTAAAATA
*
162654 AAATAGGTGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
162677 AAATAGGCGCTACATATTATGTT
1 AAATAGGCGCTACATATTATGTT
* *
162700 AAATAAGCGCTACCTATTA
1 AAATAGGCGCTACATATTA
162719 CATTAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATAGGCGCTACATATTATGTT
Found at i:162724 original size:23 final size:23
Alignment explanation
Indices: 162662--162725 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
162652 TAAAATAGGT
** *
162662 GCTACATATTATGTTAAATAGGC
1 GCTACATATTACATTAAATAAGC
**
162685 GCTACATATTATGTTAAATAAGC
1 GCTACATATTACATTAAATAAGC
*
162708 GCTACCTATTACATTAAA
1 GCTACATATTACATTAAA
162726 CTAGCTACCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (23 bp):
GCTACATATTACATTAAATAAGC
Found at i:162801 original size:22 final size:23
Alignment explanation
Indices: 162775--162822 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
162765 CGGTAAAATA
*
162775 AAATAAGCG-TACCTATTACTTT
1 AAATAAGCGCTACCTATTACGTT
162797 AAATAAGCGCTACCTATTACGTT
1 AAATAAGCGCTACCTATTACGTT
162820 AAA
1 AAA
162823 CTAGCTACCG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTACGTT
Found at i:162806 original size:97 final size:98
Alignment explanation
Indices: 162677--162920 Score: 341
Period size: 97 Copynumber: 2.5 Consensus size: 98
162667 ATATTATGTT
* * *
162677 AAATAGGCGCTACATATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCTATTTGT
1 AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTTGT
*
162742 TTAAAGATTAATAATGATGTAAACGGTAAAATA
66 TTAAAGATTAATAATAATGTAAACGGTAAAATA
*
162775 AAATA-A-GCGTACCTATTACT-TTAAATAAGCGCTACCTATTACGTTAAACTAGCTACCGATTT
1 AAATAGACGC-TACCTATTA-TGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTT
* * *
162837 GTTTAAAGGTTAATAATAATGTAAATGGTTAAATA
64 GTTTAAAGATTAATAATAATGTAAACGGTAAAATA
* * **
162872 AAATAGACGCTACTTATTATGTTAAATAGGTACTACCTATTACATTAAA
1 AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAA
162921 TAACCACTAC
Statistics
Matches: 128, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
96 2 0.02
97 85 0.66
98 39 0.30
99 2 0.02
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (98 bp):
AAATAGACGCTACCTATTATGTTAAATAAGCGCTACCTATTACATTAAACTAGCTACCGATTTGT
TTAAAGATTAATAATAATGTAAACGGTAAAATA
Found at i:162843 original size:218 final size:219
Alignment explanation
Indices: 162589--163041 Score: 649
Period size: 218 Copynumber: 2.1 Consensus size: 219
162579 AAACAGGCGT
* *
162589 TACCTATTACGTTAAACTAACTACCGGTTTGTTTAAAGGTTAATTATAAGGTAAACGGTAAAATA
1 TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
** * ** * *
162654 AAATAGGTGCTACATATTATGTTAAATAGGCGCTACATATTATGTTAAATAAGCGCTACCTATTA
66 AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
* * *
162719 CATTAAACTAGCTACCTATTTGTTTAAAGATTAATAATGATGTAAACGGTAAAATAAAATA-A-G
131 CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
*
162782 CGTACCTATTACTTTAAATAAGCGC
196 C-TACCTATTACGTTAAATAAGCGC
* * * *
162807 TACCTATTACGTTAAACTAGCTACCGATTTGTTTAAAGGTTAATAATAATGTAAATGGTTAAATA
1 TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
* * *
162872 AAATAGACGCTACTTATTATGTTAAATAGGTACTACCTATTACATTAAATAACCACTACCTATTA
66 AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
** * *
162937 TGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACG
131 CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
163002 CTACCTATTACGTTAAATAAGCGC
196 CTACCTATTACGTTAAATAAGCGC
**
163026 TATTTATTACGTTAAA
1 TACCTATTACGTTAAA
163042 TAAGCACTAC
Statistics
Matches: 207, Mismatches: 26, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
218 168 0.81
219 37 0.18
220 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (219 bp):
TACCTATTACGTTAAACTAACTACCGATTTGTTTAAAGGTTAATAATAAGGTAAACGGTAAAATA
AAATAGACGCTACATATTATGTTAAATAGGCACTACATATTACATTAAATAACCACTACCTATTA
CATTAAACTAACTACCGATTTGTTTAAAGATTAATAATAATGTAAACGGTAAAATAAAATAGACG
CTACCTATTACGTTAAATAAGCGC
Found at i:162907 original size:23 final size:23
Alignment explanation
Indices: 162881--162948 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
162871 AAAATAGACG
* ***
162881 CTACTTATTATGTTAAATAGGTA
1 CTACCTATTATGTTAAATAACCA
**
162904 CTACCTATTACATTAAATAACCA
1 CTACCTATTATGTTAAATAACCA
162927 CTACCTATTATGTTAAACTAAC
1 CTACCTATTATGTTAAA-TAAC
162949 TACCGATTTG
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
CTACCTATTATGTTAAATAACCA
Found at i:162931 original size:121 final size:121
Alignment explanation
Indices: 162775--163064 Score: 438
Period size: 121 Copynumber: 2.4 Consensus size: 121
162765 CGGTAAAATA
* * * *
162775 AAATAAGC-GTACCTATTACTTTAAATAAGCGCTACCTATTACGTTAAACTAGCTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
* * *
162839 TTAAAGGTTAATAATAATGTAAATGGTTAAATAAAATAGACGCTACTTATTATGTT
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
* * * *
162895 AAATAGGTACTACCTATTACATTAAATAACCACTACCTATTATGTTAAACTAACTACCGATTTGT
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
162960 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
66 TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
* ** *
163016 AAATAAGCGCTATTTATTACGTTAAATAAGCACTACCTATTACGTTAAA
1 AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAA
163065 TAAGCGCTAC
Statistics
Matches: 150, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
120 6 0.04
121 144 0.96
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (121 bp):
AAATAAGCACTACCTATTACATTAAATAAGCACTACCTATTACGTTAAACTAACTACCGATTTGT
TTAAAGGTTAATAATAATGTAAATGGTAAAATAAAATAGACGCTACCTATTACGTT
Found at i:163019 original size:23 final size:23
Alignment explanation
Indices: 163000--163087 Score: 140
Period size: 23 Copynumber: 3.8 Consensus size: 23
162990 ATAAAATAGA
163000 CGCTACCTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
**
163023 CGCTATTTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
*
163046 CACTACCTATTACGTTAAATAAG
1 CGCTACCTATTACGTTAAATAAG
*
163069 CGCTACATATTACGTTAAA
1 CGCTACCTATTACGTTAAA
163088 CTAACTACCG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (23 bp):
CGCTACCTATTACGTTAAATAAG
Found at i:165223 original size:20 final size:20
Alignment explanation
Indices: 165187--165224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
165177 ATCATATTCC
**
165187 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
165207 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
165225 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:166551 original size:29 final size:30
Alignment explanation
Indices: 166489--166555 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
166479 CAGAAAGCGC
*
166489 CATGTATGAAATTGAGAAATTTTAAACATT
1 CATGTATGAAATTGAGAAATTGTAAACATT
**
166519 -ATGTATGAAATTGA-AAATTAGTATGC-TT
1 CATGTATGAAATTGAGAAATT-GTAAACATT
166547 CATGTATGA
1 CATGTATGA
166556 GTGAGTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (30 bp):
CATGTATGAAATTGAGAAATTGTAAACATT
Found at i:172246 original size:27 final size:25
Alignment explanation
Indices: 172189--172253 Score: 67
Period size: 27 Copynumber: 2.5 Consensus size: 25
172179 AATGAAAGTT
172189 ATAATTTAAGGAAAAAAAATAATTA
1 ATAATTTAAGGAAAAAAAATAATTA
* ** *
172214 AAAATTTAAGGATTAATTAAATAATTC
1 ATAATTTAAGGA--AAAAAAATAATTA
*
172241 ATAATTTAGGGAA
1 ATAATTTAAGGAA
172254 TATGATGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 12 0.38
27 20 0.62
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (25 bp):
ATAATTTAAGGAAAAAAAATAATTA
Done.